Dandelion Racing driver Makino, who topped practice earlier on Saturday, posted a best lap of 1m22.063s at the end of the Q2 pole shootout to eclipse Team Mugen rival Lawson by 0.179 seconds.
It marks Makino’s first pole position since he made his Super Formula debut at Suzuka back in 2019.
His rookie team-mate Kakunoshin Ota underlined Dandelion’s turnaround by qualifying in third – as well as qualifying top of his Q1 group.
Ren Sato made it an all-Honda top four in his best qualifying performance of the year for Nakajima Racing, with championship leader Ritomo Miyata (TOM’S) the best of the Toyota runners in fifth.
Two bonus points for Lawson mean that Miyata heads into Sunday’s race with a reduced 10-point cushion at the head of the drivers’ standings.
Joining Miyata on the third row will be Naoki Yamamoto, completing a strong showing from Nakajima.
Reigning two-time champion Tomoki Nojiri could manage no better than seventh place, six tenths off pole, ahead of Kenta Yamashita (Kondo Racing) and Hiroki Otsu, who is deputising for an injured Toshiki Oyu at TGM Grand Prix.
Title contender Sho Tsuboi was a disappointing 11th, immediately behind Inging team-mate Sena Sakaguchi.
Impul didn’t get either of its drivers through to Q2, with Yuhi Sekiguchi lining up 13th and Ryo Hirakawa languishing down in 20th with the second-slowest time in his Q1 group.
Ukyo Sasahara, making his first race appearance of the year for TOM’S after being handed Giuliano Alesi’s seat for the rest of the season, was also eliminated in Q1 and will start 16th.